Joe probably has more sound advice than I, but in my sig., in the write-up it has rear main removal and installation....
Yeah, there are three holes that the dowel pins go in. There is only 3 holes that have a 'stop' down in the hole. Take a look at the flywheel when you get it off and you will see 3 holes the same distance from each other in a triangle form. They have 'stops' half way down the hole and the other holes do not. You can use a small hammer and tap them into the stops...
The dowel pins are to align the pressure plate over the flywheel...
Good Luck
Edit: I had a stock clutch and a King Cobra, I would venture to say it is 20-25% stiffer

, but my memory may be incorrect...if anyone else has more recently, post up...but the King Cobra is very 'stop and go'able"